Why would my 01 yz 125 flood out i just put a third new top end on and it floods out and the piston goes bad

Have you made any airbox or exhaust modifications? (too oily air filter, clogged chamber, dented header)
Are you running stock carby/jets? Using the correct range sparkplug?
Check condition of reeds, they may have relaxed their tension and are remaining open, or been damaged by carbon blowback.
Are you using the right fuel at the correct ratio?
Are your crank seals in good condition (is there any sign of fuel oil weeping from behind magneto?
Are the conrod and crank pins okay? (excessive piston side play or up down freeplay)
Is your ignition providing a healthy spark? (coil condition and good earth)
All these issues can have a bearing on your problem, goodluck.
Cheers!